Microbial Natural Products as Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro)

Abstract

The main protease (M^pro) of the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was subjected to hyphenated pharmacophoric-based and structural-based virtual screenings using a library of microbial natural products (>24,000 compounds). Subsequent filtering of the resulted hits according to the Lipinski's rules was applied to select only the drug-like molecules. Top-scoring hits were further filtered out depending on their ability to show constant good binding affinities towards the molecular dynamic simulation (MDS)-derived enzyme's conformers. Final MDS experiments were performed on the ligand-protein complexes (compounds 1-12, Table S1) to verify their binding modes and calculate their binding free energy. Consequently, a final selection of six compounds (1-6) was proposed to possess high potential as anti-SARS-CoV-2 drug candidates. Our study provides insight into the role of the M^pro structural flexibility during interactions with the possible inhibitors and sheds light on the structure-based design of anti-coronavirus disease 2019 (COVID-19) therapeutics targeting SARS-CoV-2.

Keywords: Covid-19; Mpro; SARS-CoV-2; docking; microbial natural products; molecular dynamic simulation.

Figure 1

Applied strategy in the present study.

Figure 2

(A): The main domains (M^pro) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Brick red: Domain I, Golden yellow: Domain II, Cyan: Domain III), (B): Heat-map illustrating the flexible regions on SARS-CoV-2 M^pro, (C): The active site volume changes during the course of molecular dynamic simulation (MDS) (D and E): root main square deviation (RMSD) and root main square fluctuation (RMSF) of SARS-CoV-2 M^pro after 25 ns of MDS.

Figure 3

Generated pharmacophore models (B and D) according to the previously reported co-crystalized ligands (7 and 8, A and C). Gray spheres indicate hydrogen bond donors, orange spheres indicate hydrogen bond acceptors, and green spheres indicate hydrophobic centers. Green amino acid residues represent the S1 pocket, blue amino acid residues represent the S2 pocket, yellow amino acid residues represent the S3 and S4 pockets in the M^pro active site (A and C).

Figure 4

Top-scoring compounds (1–6) retrieved from the in silico virtual screening on the M^pro active site along with the co-crystallized inhibitors 7 and 8 in addition to the previously reported antiviral microbial natural products (9–12).

Figure 5

Interactions and binding modes of compounds 1 and 2 (Blue and red molecules, respectively) inside the M^pro active site in the crystal form and during MDS (1-A–2-F).

Figure 6

Interactions and binding modes of compounds 3 and 4 (Blue and red molecules, respectively) inside the M^pro active site in the crystal form and during MDS (3-A–4-F).

Figure 7

Interactions and binding modes of compounds 5 and 6 (Blue and red molecules, respectively) inside the M^pro active site in the crystal form and during MDS (5-A–6-F).